ADL: generate pdbqt from pdb with metal

Paul Rigor (uci) paul.rigor at uci.edu
Mon Mar 8 19:06:55 PST 2010


Hi,

I'm trying to prepare a ligand using the distributed prepare_ligand4.py
script.  The pdb structure however contains an iron metal.   Why is
everything but the metal getting erased? Basically, a ring structure with a
coordinated Fe is rendered as just the Fe.

What's the best way to prepare a ligand coordinated with a metal?

Thanks,
Paul


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